GeneBe

LPCAT1

protein-coding

lysophosphatidylcholine acyltransferase 1, the group of MicroRNA protein coding host genes|EF-hand domain containing|1-acylglycerol-3-phosphate O-acyltransferases

Gene summary

This gene encodes a member of the 1-acyl-sn-glycerol-3-phosphate acyltransferase family of proteins. The encoded enzyme plays a role in phospholipid metabolism, specifically in the conversion of lysophosphatidylcholine to phosphatidylcholine in the presence of acyl-CoA. This process is important in the synthesis of lung surfactant and platelet-activating factor (PAF). Elevated expression of this gene may contribute to the progression of oral squamous cell, prostate, breast, and other human cancers. [provided by RefSeq, Sep 2016]

Previous symbols:
  • AYTL2

MANE transcript

NM_024830.5

Inheritance

—

ClinVar variants

U:84B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr5:1,456,480-1,524,282

External References & Databases

Ensembl (ENSG00000153395)NCBI Gene (79888)OMIM (610472)HGNC:25718GenCCUniProt (Q8NF37)AlphaFoldClinVar (LPCAT1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~67.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to LPCAT1 variants in ClinVar

2 Conditions Cataloged
not specifiedTotal: 80
not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024830.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
2
clinvar
 3
missense
79
clinvar
5
clinvar
 84
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
4
clinvar
 4
Total00845291
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_024830.5RefSeqNP_079106.314MANE Select
ENST00000283415.4EnsemblENSP00000283415.314MANE Select
ENST00000475622.5EnsemblENSP00000423472.114Standard
ENST00000475622.6EnsemblENSP00000423472.114Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Ether lipid metabolism - Homo sapiens (human)
  • Glycerophospholipid metabolism - Homo sapiens (human)
  • Neutrophil degranulation
  • Acyl chain remodelling of PG
  • Metabolism of lipids

Biological Process

  • phosphatidic acid biosynthetic process
  • phosphatidylcholine biosynthetic process
  • phospholipid biosynthetic process
  • phosphatidylglycerol acyl-chain remodeling
  • phosphatidylcholine acyl-chain remodeling

Molecular Function

  • 1-acylglycerol-3-phosphate O-acyltransferase activity
  • calcium ion binding
  • 2-acylglycerol-3-phosphate O-acyltransferase activity
  • 1-alkenylglycerophosphocholine O-acyltransferase activity
  • 1-acylglycerophosphocholine O-acyltransferase activity

Cellular Component

  • Golgi membrane
  • endoplasmic reticulum
  • endoplasmic reticulum membrane
  • Golgi apparatus
  • lipid droplet

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000283415
Coding exons
14
Length
67498
Individuals with no LoFs
125734
Homozygous LoFs
0
Heterozygous LoFs
13
Defined
125747
p
0.0000517
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.612543370.7530.00002333417
Missense (PolyPhen)74131.760.561621261
Synonymous-1.071671501.110.00001181118
Loss of Function3.62727.50.2550.00000154293

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000190.00018rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000890.000079rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Possesses both acyltransferase and acetyltransferase activities (PubMed:16864775, PubMed:21498505). Activity is calcium-independent (By similarity). Mediates the conversion of 1- acyl-sn-glycero-3-phosphocholine (LPC) into phosphatidylcholine (PC) (PubMed:21498505). Displays a clear preference for saturated fatty acyl-CoAs, and 1-myristoyl or 1-palmitoyl LPC as acyl donors and acceptors, respectively (PubMed:16704971). May synthesize phosphatidylcholine in pulmonary surfactant, thereby playing a pivotal role in respiratory physiology (PubMed:16864775). Involved in the regulation of lipid droplet number and size (PubMed:25491198). {ECO:0000250|UniProtKB:Q3TFD2, ECO:0000269|PubMed:16864775, ECO:0000269|PubMed:21498505, ECO:0000269|PubMed:25491198}.;

Recessive Scores

pRec
0.166

Intolerance Scores

LoFtool
0.146
RVIS EVS
-0.84
RVIS percentile EVS
11.4

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.638

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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